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adeft

Tool for disambiguating acronyms and abbreviations in text for NLP applications

askee-august-2021-demo-model-collection

bioagents

Biological reasoning agents

biobert

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

chatbot

This program leverages Natural Language Programming framework spacy.io to build simple conversations on a given topic.

cookiecutter

A command-line utility that creates projects from cookiecutters (project templates), e.g. Python package projects, jQuery plugin projects.

cookiecutter-luigi-aws

covid-19

Scripts and other utilities relevant to the CORD-19 dataset

depmap_analysis

dianakolusheva.github.io

emmaa

Ecosystem of Machine-maintained Models with Automated Analysis

gilda

Grounding of biomedical named entities with contextual disambiguation

indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

indra_apps

indra_cogex

INDRA Context Graph Extension

indra_db

A Database-based knowledge back-end built on and for INDRA. The INDRA Database is a service that can be set up by any user with their own content and knowledge access. Our implementation of the database is the back-end to many of our projects, providing a vast and detailed knowledge base derived from many resources.

indra_db_docker

Home to the docker file used on AWS for the indra_db tools.

indra_docker

Docker build for INDRA, REACH, PySB, and related dependencies.

indra_pathway_map

indra_reading

Tools used for large scale reading, mostly using AWS Batch.

indra_world

INDRA World Modelers services

indralab-vue

A package of Vue Components for use in Indralab web services.

ontologies

Ontologies for the World Modelers system

protmapper

Map amino acid sites of post-translational modifications from models or data to reference positions.

pubmed_abstract

pykqml

KQML messaging library

pysb

Python framework for Systems Biology modeling

reach

Reach Biomedical Information Extraction

ui_util

This repo creates general utilities for our user interfaces.